4.2 Web and Local Connections

Before you can use the search & download feature it may be necessary to configure the link between the MembraneEditor and the Protein Data Bank. This can be done by opening 'Connection Settings' , located inside the 'Settings' menu in the menu bar.

The appearing dialog inherits 2 categories: -'Connection', where you perform your settings with regards to the internet connection and -'RCSB Links', where you can edit the URLs that are used.

Configure Connection

By default, the program uses a direct internet connection. In case your connection uses a proxy, you may have to do some configurations. Choose 'Manual proxy configuration' to enable proxy use.

Use the fields in 'Authentification' in order to enter an username and a password; use the fields in 'Address' to enter an IP address and a port number for http and ftp proxy access.

It may be necessary to fill in some fields depending on your system. You can, however test your settings by pressing 'Test Configuration'. The test may take a few seconds and informs you if both http and ftp access can be established.

Note that the http protocol is used for downloading a pdb file from the PDB. Without access, this feature is not available. Ftp access is required for updating the index file.

Edit RCSB Links

Certain URLs are required in order to link with the Protein Data Bank. Those links are already defined and should work currently. It is possible that the structure of the RCSB site, and therefore those links may change eventually. In this case, you will have to find out the proper links and replace the old ones, using the textfields located in the 'RCSB Links' tab.

There are 4 different URLs used by this program and two additional links to local tools:

Download Link

Used to retrieve the specified pdb file when using the download function

Entries File

Points on the index file used for the search function. Only required for updating

Preview Image

The location of the preview image that is shown when selecting a search result

Info Page

Links to a specified info page of a pdb file that may be opened in your system browser

Jmol Execution Environment

Link to Jmol on your local file system. This must only be changed if you have a new or a custom version of Jmol on your local system, otherwise, the pre-installed Jmol in the Cm2 folder will be used